The period that followed was spent studying philosophy at the École Normale Supérieure in Paris (coinciding with the events of May 1968), and as a law student at Edinburgh University, where he received the Green Prize. Despite being called to the bar in 1972, MacGregor next decided to take an art history degree. The following year, on a Courtauld Institute (University of London) summer school in Bavaria, the Courtauld's director Anthony Blunt spotted MacGregor and persuaded him to take a master's degree under his supervision.[2] Blunt later considered MacGregor "the most brilliant pupil he ever taught".[3]

In 1987 MacGregor became a highly successful director of the National Gallery in London. There he was dubbed "Saint Neil", partly because of his popularity at that institution and partly because of his devout Christianity, and the nickname stuck after his departure from the Gallery. During his directorship, MacGregor presented three BBC television series on art: Painting the World in 1995, Making Masterpieces, a behind-the-scenes tour of the National Gallery, in 1997 and Seeing Salvation, on the representation of Jesus in western art, in 2000. He declined the offer of a knighthood in 1999, the first director of the National Gallery to do so.[5]

MacGregor was made director of the British Museum in August 2002, at a time when that institution was £5 million in deficit. He has been lauded for his "diplomatic" approach to the post, though MacGregor rejects this description, stating that "diplomat is conventionally taken to mean the promotion of the interests of a particular state and that is not what we are about at all".[5] Holding his office during a period which has seen the Acropolis Museum constructed in Athens, he has consistently argued against returning the British Museum's sculptures from the Parthenon (the "Elgin Marbles") to Greece. He has stated that it is the British Museum's duty to "preserve the universality of the marbles, and to protect them from being appropriated as a nationalistic political symbol"[6] and that "there is no legal system in Europe that would challenge the [British Museum's] legal title" to the works.[7]

MacGregor has made many programmes for British television and radio. In the year 2000, he presented on television Seeing Salvation, about how Jesus had been depicted in famous paintings. More recently, he has made important contributions on BBC Radio Four, including A History of the World in 100 Objects and, in 2012, a series of fifteen-minute programmes after The World at One called Shakespeare's Restless World, discussing themes in the plays of William Shakespeare.[11]

At the end of September 2014 UK domestic transmission started of his similarly formatted Talk Radio series Germany: Memories of a Nation.[12]